Research workbench
Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor DR718A
Analyse Structure of plasmepsin II from plasmodium falciparum complexed with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z22
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin-2
- UniProt
- W7FL77
- Ligands
- 4KG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin-2 | protein | 329 | 13% helix, 47% strand | W7FL77 |
Ligands and binding sites
- 4KG · 2-amino-7-phenyl-3-{[(2R,5S)-5-phenyltetrahydrofuran-2-yl]methyl}quinazolin-4(3H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.75 | 0.86 | 54 | empty |
| 2 | 302 | 0.74 | 0.86 | 43 | empty |
| 3 | 124 | 0.68 | 0.89 | 22 | empty |
| 4 | 81 | 0.46 | 0.81 | 18 | empty |
| 5 | 78 | 0.40 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1250 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4Z22 · structure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor DR718A · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt W7FL77
- Elsewhere: RCSB PDB 4Z22 · PDBe 4Z22 · UniProt W7FL77
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